Contacts of the strand formed by residues 158 - 164 (chain M) in PDB entry 6CNB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 158 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B ASP* 4.7 3.0 - - - +
543B LEU* 3.2 37.0 - - + +
155M ASN* 2.6 55.3 + - - +
156M ASN 3.1 5.9 + - - +
157M GLY* 1.3 76.9 - - - +
159M TYR* 1.3 67.5 + - - +
173M ILE* 3.2 32.8 + - + +
174M GLU 4.8 1.4 + - - +
176M VAL* 3.8 15.6 - - - +
307N PHE 3.7 7.2 - - - +
308N GLN* 4.0 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 159 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157M GLY* 3.2 34.1 + - - +
158M GLN* 1.3 82.9 - - - +
160M ALA* 1.3 58.7 + - - +
170M LEU* 3.4 40.4 - - + -
171M VAL 3.2 7.2 - - - +
172M PRO* 3.4 30.1 - - + -
173M ILE* 3.4 6.6 - - - +
306N VAL* 3.2 2.9 - - - +
307N PHE* 2.6 42.8 + - + +
308N GLN 5.3 0.2 - - - -
309N LEU* 3.7 27.6 - - + -
310N PRO 5.7 0.7 + - - -
313N LEU* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M LEU* 3.9 29.4 - - + -
159M TYR* 1.3 75.9 - - - +
161M ALA* 1.3 67.4 + - - +
170M LEU* 3.3 4.7 - - - +
171M VAL* 2.9 30.1 + - + +
173M ILE* 3.4 9.8 - - + +
304N PHE* 4.9 13.5 - - + -
305N MET 3.5 0.7 - - - -
306N VAL* 3.6 20.4 - - + -
307N PHE* 5.6 0.2 - - - -
396N ALA* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M ALA* 1.3 78.7 - - - +
162M PHE* 1.3 63.8 + - - +
168M VAL* 4.3 13.2 - - + -
169M TYR 3.1 15.5 - - - +
170M LEU* 4.0 6.1 - - + -
171M VAL* 4.6 0.9 - - - +
304N PHE* 3.2 13.1 - - - +
305N MET* 2.7 37.1 + - + +
307N PHE* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M ALA* 1.3 78.5 - - - +
163M VAL* 1.3 66.1 + - - +
164M LYS* 3.6 26.6 + - + -
168M VAL* 3.4 3.5 - - - +
169M TYR* 2.9 79.6 + + + -
171M VAL* 4.5 11.0 - - + -
254M GLN* 3.2 30.5 - - + -
255M PHE* 4.7 10.3 - + - -
258M THR* 3.6 9.6 - - + -
300N LYS* 6.1 0.4 - - + -
301N PRO 6.2 0.4 - - - +
303N ARG 4.0 7.9 - - - +
304N PHE* 3.5 30.7 - + + +
305N MET* 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M PHE* 1.3 75.7 - - - +
164M LYS* 1.3 58.3 + - - +
165M ASP 3.3 21.8 - - - +
166M MET 5.4 0.4 - - - -
167M GLN 3.6 8.5 - - - +
168M VAL* 3.6 23.6 - - + -
294N LEU* 4.3 20.2 - - + +
295N LYS* 6.1 0.4 - - - -
297N MET* 3.0 38.4 + - + +
298N ASN* 3.7 9.0 - - - +
299N ASN 2.9 24.9 - - - +
300N LYS* 4.3 1.7 - - - +
303N ARG 5.0 2.0 + - - -
305N MET* 5.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M PHE* 3.6 23.8 + - + -
163M VAL* 1.3 70.2 - - - +
165M ASP* 1.3 67.8 + - - +
167M GLN* 2.7 58.8 + - - +
169M TYR* 3.9 10.3 - - + -
255M PHE* 3.1 53.5 - - - +
256M LYS* 5.7 0.2 - - - +
259M ILE* 3.6 29.9 - - + +
300N LYS* 3.3 28.3 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il